plotTE {ribosomeProfilingQC} | R Documentation

## Plot translational efficiency

### Description

Scatterplot of RNA/RPFs level compared to the translational efficiency.

### Usage

    plotTE(
      TE,
      sample,
      xaxis = c("mRNA", "RPFs"),
      removeZero = TRUE,
      log2 = TRUE,
      breaks.length = 50,
      ...
    )

### Arguments

`TE` | Output of translationalEfficiency
`sample` | character(1). Sample name to plot.
`xaxis` | What to plot for x-axis.
`removeZero` | Remove the 0 values from plots.
`log2` | Do log2 transform or not.
`breaks.length` | Length of breaks for histogram.
`...` | Parameters pass to plot.

### Value

A invisible data.frame with x, y of points.

### Examples

    path <- system.file("extdata", package="ribosomeProfilingQC")
    #RPFs <- dir(path, "RPF.*?\.[12].bam$", full.names=TRUE)
    #RNAs <- dir(path, "mRNA.*?\.[12].bam$", full.names=TRUE)
    #gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
    #cnts <- countReads(RPFs, RNAs, gtf, level="gene")
    cnts <- readRDS(file.path(path, "cnts.rds"))
    fpkm <- getFPKM(cnts)
    te <- translationalEfficiency(fpkm)
    plotTE(te, 1)

[Package ribosomeProfilingQC version 0.99.9 Index]